[ITK-users] (R wrapping/SimpleITK) AddCommand to ImageRegistrationMethod bug

Richard Beare richard.beare at gmail.com
Fri Apr 15 17:44:59 EDT 2016 

Also, we're working on the help for the R side, but it will also be a
translation of the C++ documentation, which is thus the canonical list.
Check that doc out at
http://www.itk.org/SimpleITKDoxygen09/html/classes.html

A high proportion of those classes are available via the wrappers.

On Fri, Apr 15, 2016 at 11:55 PM, Bradley Lowekamp <brad at lowekamp.net>
wrote:

> Hi!
>
> Glad to hear you go it working.
>
> SimpleITK wraps the majority of ITK’s image filters, it is however not a
> complete instantiation of all of ITK. If you find that there are missing
> filters or functionality that you need please post.
>
> Enjoy!
> Brad
>
> On Apr 15, 2016, at 9:15 AM, Fethallah Benmansour <fethallah at gmail.com>
> wrote:
>
> Thanks Richard.
> Followed your advice and found my way. The example script works like a
> charm :-)
> Are all the itk filters now callable from R, or just a subset ? how can I
> know this ?
> Thanks for all the great effort.
>
> --
> Fethallah
>
>
> On Thu, Apr 14, 2016 at 11:26 PM, Richard Beare <richard.beare at gmail.com>
> wrote:
>
>> You ought to be OK with bison - can you get that?
>>
>> The latest version of simpleitk on the github site have support for
>> building swig from github,so you can avoid the manual build. On all the
>> systems I've tested it is bison that appears to be used in the early stages
>> of swig building.
>>
>> On Fri, Apr 15, 2016 at 6:57 AM, Fethallah Benmansour <
>> fethallah at gmail.com> wrote:
>>
>>> Hi there,
>>>
>>> Any chance to get it to work on a Redhat 6.3 ?
>>> The current blocker is yacc, which I couldn't install with yum (EPEL
>>> enabled).
>>>
>>> Thanks,
>>>
>>> --
>>> Fethallah
>>>
>>> On Mon, Apr 11, 2016 at 5:14 PM, Bradley Lowekamp <brad at lowekamp.net>
>>> wrote:
>>>
>>>> Hello,
>>>>
>>>> We have R tested with SimpleITK on a number of systems each night. And
>>>> this morning we have run the tests on several systems, and it is running
>>>> and passing OK, this was with what every old R version was on the systems
>>>>
>>>> We should focus on getting the tests to pass on your system first. It’s
>>>> a good sign that you can run the AddCommand with the sitk::Command class.
>>>> Does the rest of the R tests pass when you run ctest?
>>>>
>>>> I am still suspicious you are not running the latest development
>>>> version. What is the git hash you are using?
>>>>
>>>> As you were digging into the SimpleITK R code you were on the right
>>>> track with the ProccessObject::AddCommand and the sitk::Command class. The
>>>> other two parts you are missing is the RCommand C++ class [1], and the
>>>> overridden ProcessObject::AddCommand method [2]. These were recently added
>>>> to SimpleITK since the 0.9 release. You can see that the added procedure
>>>> wraps the passed callable, into the RCommand class.
>>>>
>>>> HTH,
>>>> Brad
>>>>
>>>>
>>>> [1]
>>>> https://github.com/SimpleITK/SimpleITK/blob/master/Wrapping/R/sitkRCommand.h
>>>> [2]
>>>> https://github.com/SimpleITK/SimpleITK/blob/2ffffba589b24465a09eed1303bbffd6fe3fe18e/Wrapping/R/R.i#L565-L589
>>>>
>>>> On Apr 11, 2016, at 3:59 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
>>>> wrote:
>>>>
>>>> I tried running the code below as suggested - both in RStudio and the
>>>> terminal - and get the same abort/segfault error.
>>>>
>>>> Which version of R are you running? - I can install an older version to
>>>> see if it works.
>>>>
>>>> On 11 Apr 2016, at 01:02, Richard Beare <richard.beare at gmail.com>
>>>> wrote:
>>>>
>>>> This is a long shot, but lets try testing whether it is the R garbage
>>>> collection causing issues. Modify the test so that every method call result
>>>> is assigned to a different variable:
>>>>
>>>> e.g.
>>>>
>>>> a1 <- gaussian$SetVariance(2)
>>>> a2 <- gaussian$AddCommand( 'sitkStartEvent',  f1 )
>>>> a3 <- gaussian$AddCommand( 'sitkEndEvent', f2 )
>>>>
>>>> I was running in a terminal on my mac, with an older version of R.
>>>>
>>>>
>>>> On Mon, Apr 11, 2016 at 9:56 AM, Mathew Guilfoyle <
>>>> mrguilfoyle at gmail.com> wrote:
>>>>
>>>>> Richard
>>>>>
>>>>> It seems it must be something specific to my setup.  I ran your
>>>>> example and get the same hard abort in Rstudio.  Running the example in
>>>>> R.app I get the same error but a  somewhat more graceful crash with the
>>>>> following error message:
>>>>>
>>>>> gaussian$AddCommand( 'sitkStartEvent',  f1 )
>>>>>
>>>>>  *** caught segfault ***
>>>>> address 0x7ff511000080, cause 'memory not mapped'
>>>>>
>>>>> Traceback:
>>>>>  1: .Call("R_swig_ProcessObject_AddCommand", self, event, cmd,
>>>>> as.logical(.copy),     PACKAGE = "SimpleITK")
>>>>>  2: f(x, ...)
>>>>>  3: gaussian$AddCommand("sitkStartEvent", f1)
>>>>>
>>>>> Possible actions:
>>>>> 1: abort (with core dump, if enabled)
>>>>> 2: normal R exit
>>>>> 3: exit R without saving workspace
>>>>> 4: exit R saving workspace
>>>>>
>>>>> I have tried the version of SimpleITK built without the version of
>>>>> SWIG you patched to correct the character argument error, again I get the
>>>>> same behaviour.
>>>>>
>>>>> Bradley - I’m using the latest SimpleITK 0.9 source compiled using the
>>>>> super build on OS X 10.11.  I’ve done the build with the supplied SWIG and
>>>>> with a version patched by Richard and available here:
>>>>> https://github.com/richardbeare/swig.git.  I’m funning R 3.2.4 in
>>>>> Rstudio IDE.
>>>>>
>>>>>
>>>>>
>>>>> On 10 Apr 2016, at 23:17, Bradley Lowekamp <brad at lowekamp.net> wrote:
>>>>>
>>>>> Hello,
>>>>>
>>>>> I would like to know your environment.
>>>>>
>>>>> What version of SimpleITK?  R? OS? Compiler? Did you use simpleITK's
>>>>> super build? If not what version of SWIG?
>>>>>
>>>>> Thanks
>>>>>
>>>>> On Apr 10, 2016, at 9:46 AM, Mathew Guilfoyle <mrguilfoyle at gmail.com>
>>>>> wrote:
>>>>>
>>>>> Richard
>>>>>
>>>>> Thanks for the reply.  I hadn't appreciated that function being passed
>>>>> in the registration example was a closure.  However, in the
>>>>> FiterProgressReporting example it is not a closure.
>>>>>
>>>>> I have modified my code to be a closure but still get a crash/abort; I
>>>>> have also run the code in the examples themselves verbatim and get the same
>>>>> problem.
>>>>>
>>>>> Any further ideas on how to get this working?
>>>>>
>>>>> Cheers
>>>>>
>>>>>
>>>>> On 10 Apr 2016, at 02:10, Mathew Guilfoyle <mrguilfoyle at gmail.com>
>>>>> wrote:
>>>>>
>>>>> There seems to be a problem with using the $AddCommand function to
>>>>> ImageRegistrationMethod objects in the R wrapping to SimpleITK.
>>>>>
>>>>> Using R 3.2.4 on OS X 10.11
>>>>>
>>>>> Example:
>>>>>
>>>>> f <- function(x){print(x$GetMetricValue())}
>>>>>
>>>>> registration = ImageRegistrationMethod()
>>>>>
>>>>> registration$AddCommand(‘sitkIterationEvent’, f(registration))
>>>>>
>>>>> This last line causes R to abort/hard crash (no error message).  This
>>>>> behaviour is irrespective of which event type I use or the function passed
>>>>> as the second argument (e.g. even something simple like print(‘Hello’))
>>>>>
>>>>> The AddCommand method is inherited from the SimpleITK ProcessObject
>>>>> type.  Digging around in the SimpleITK.R file I can see that the
>>>>> ProcessObject$AddCommand method expects a second argument of type
>>>>> ‘_p_itk__simple__Command’.
>>>>>
>>>>> There is a ‘Command’ method that generates a new object of type
>>>>> ‘_p_itk__simple__Command’.  If I pass this resulting object as the second
>>>>> argument to registration$AddCommand then I do not get an error.  However,
>>>>> there doesn’t seem to be any way to point the ‘_p_itk__simple__Command’
>>>>> object to my function or otherwise convert my function to a
>>>>> ‘_p_itk__simple__Command’ type.
>>>>>
>>>>> The $AddCommand method is used in a couple of example scripts on the
>>>>> SimpleITK site (using it for monitoring a registration and a filter e.g.
>>>>> https://github.com/SimpleITK/SimpleITK/blob/master/Examples/FilterProgressReporting.R)
>>>>> so I don’t know if it was working previously and a bug has been introduced
>>>>> more recently? (the example scripts cause the same error when I run them
>>>>> now)
>>>>>
>>>>>
>>>>> _____________________________________
>>>>> Powered by www.kitware.com
>>>>>
>>>>> Visit other Kitware open-source projects at
>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>
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>>>>> http://www.kitware.com/products/protraining.php
>>>>>
>>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>>>
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>>>>>
>>>>>
>>>>>
>>>>
>>>> _____________________________________
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>>>> Visit other Kitware open-source projects at
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>>>> Kitware offers ITK Training Courses, for more information visit:
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>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
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>>>>
>>>>
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>>
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>>
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>>
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
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>>>
>>
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>
> Visit other Kitware open-source projects at
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.php
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
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